Biology subjects

Flint, L.

Publications and source records attributed to Flint, L..

5 recordsLinked to original sources

bioRxiv2026

SMEW: An interactive multi-scale toolkit for cross-condition and network-based analysis of spatial metabolomics data

Spatial metabolomics, measured through mass spectrometry imaging (MSI), provides high-throughput, spatially resolved information on metabolite distributions within tissues, including endogenous metabolites and exogenous compounds. This offers a direct readout of cellular biochemical activity and phenotypes, not fully captured by transcriptomics or proteomic profiling. However, inferring biologically meaningful patterns from noisy, high-dimensional MSI data, particularly across multiple samples and complex experimental designs, remains challenging, and often requires substantial programming expertise. Here we introduce SMEW (Spatial Metabolomics Enhanced Workflow), a flexible, interactive and shareable Shiny-based platform designed to enable code-free downstream analysis of spatial metabolomics MSI data. SMEW provides a unified environment for hierarchical analysis across bulk-, region- and pixel-level resolutions, allowing comparisons between experimental conditions like disease or treatment groups while highlighting coherent metabolic patterns and linking these patterns to biological pathways. The workflow leverages local spatial covariation to robustly summarise MSI data through dimensionality reduction, clustering and identification of spatially variable metabolites. In addition, metabolite co-localisation and covariation network analysis, together with spatially resolved pathway enrichment facilitate the biological interpretation of cross-condition datasets within a single integrated interface. SMEW is applicable across MSI technologies and mass resolutions, as illustrated through case studies on DESI and MALDI-ToF datasets from lung, liver, and kidney. By complementing existing MSI processing and visualisation tools with an accessible, multi-sample, and biologically interpretable analysis framework, SMEW enables functional, flexible, rigorous and intuitive exploration of spatial metabolomics datasets. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/721059v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1e2abaeorg.highwire.dtl.DTLVardef@753ee9org.highwire.dtl.DTLVardef@1756fc1org.highwire.dtl.DTLVardef@fbedc7_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LISMEW provides a flexible, interactive and shareable Shiny-based platform designed to enable code-free downstream analysis of spatial metabolomics MSI data C_LIO_LIThe SMEW framework enables hierarchical analysis at bulk-, region- and pixel levels within a unified framework without relying on extensive programming expertise C_LIO_LIThe pipeline integrates spatially aware clustering, pathway analysis and identification of metabolite co-localisation modules C_LIO_LIThe workflow facilitates flexible comparison of multi-sample experimental conditions through multivariate modelling, differential testing and covariation networks to study treatment- and disease-associated metabolite dynamics C_LIO_LISMEW has been applied to interrogate diverse biological questions, including characterising disease-associated remodelling in a mouse bleomycin model of pulmonary fibrosis, exploring the therapeutic index of antisense oligonucleotides in the liver and assessing metabolic heterogeneity in a small molecule-treated mouse renal tumour model C_LI

bioinformatics↗

bioRxiv2024

Genome-wide CRISPRa screens nominate modulators of CAR T cell survival within distinct tumor cytokine milieus

Chimeric Antigen Receptor (CAR) T cell therapy has revolutionized the treatment of B cell malignancies and translating this success to other cancers remains an ongoing clinical objective. Next-generation T cell products in development aim to genetically modulate many facets of cell behavior, for which gene-nominating platforms provide a useful framework for prioritization. Among competing screening approaches, CRISPR activation (CRISPRa) technology permits gain-of-function (GoF) gene surveys at genome-wide scale, but routine implementation in primary T cells has been stymied by high cell requirements ([~]107 - 108) and abbreviated activity. Here, we describe a novel cell manufacturing schema using an all-in-one transposon-based gene delivery system coupled with CAR-restricted cell expansion to generate yields (109) of primary T cells bearing CAR and CRISPRa transgenes that are well above the threshold needed for genome-scale screening. CRISPRa activity is sustained via the inclusion of divergent, duplicate Elongation Factor 1 core/human T-cell leukemia virus (EF1-HTLV) hybrid promoters; while guide RNA representation is preserved through late lentiviral transduction, thus preventing bottlenecking and premature candidate pruning. CRISPRa-CAR T cells manufactured via this pipeline retain potent on-target gene-overexpression (>85% target+) across varied cell subsets (e.g. Tim-3+Lag3+ or serial-challenge) and timescales (>14 days). When deployed to survival-based genome-wide selection landscapes, CRISPRa-CAR pools nominate known and novel endogenous genes capable of enhancing CD8+ CAR T survival in cytokine-rich (e.g. MYC, FUT6, IRF4, GSE1) and cytokine-depleted (e.g. CSF2RB, STAT6, IRF4, GSE1) settings of tumor challenge. This system will have broad utility for therapy-enhancing gene discovery.

immunology↗

bioRxiv2021

Triazolopyrimidines target aerobic respiration in Mycobacterium tuberculosis

We previously identified a series of triazolopyrimidines with anti-tubercular activity. We determined that Mycobacterium tuberculosis strains with mutations in a component of the cytochrome bc1 system (QcrB) were resistant to the series. A cytochrome bd oxidase deletion strain was also more sensitive to this series. We isolated resistant mutants, all of which had mutations in Rv1339. Compounds were active against intracellular bacteria but did not inhibit mitochondrial respiration in human HepG2 cells. These data are consistent with triazolopyrimidines acting via inhibition of M. tuberculosis QcrB.

microbiology↗

bioRxiv2021

Identification of novel chemical scaffolds that inhibit the growth of Mycobacterium tuberculosis in macrophages

Mycobacterium tuberculosis is an important global pathogen for which new drugs are urgently required. The ability of the organism to survive and multiply within macrophages may contribute to the lengthy treatment regimen with multiple drugs that are required to cure the infection. We screened the MyriaScreen II diversity library of 10,000 compounds to identify novel inhibitors of M. tuberculosis growth within macrophage-like cells using high content analysis. Hits were selected which inhibited the intramacrophage growth of M. tuberculosis without significant cytotoxicity to infected macrophages. We selected and prioritized compound series based on their biological and physicochemical properties and the novelty of the chemotypes. We identified five chemical classes of interest and conducted limited catalog structure-activity relationship studies to determine their tractability. We tested activity against intracellular and extracellular M. tuberculosis, as well as cytoxicity against murine RAW264.7 and human HepG2 cells. Benzene amide ethers, thiophene carboxamides and thienopyridines were only active against intracellular bacteria, whereas the phenylthiourea series was also active against extracellular bacteria. One member of a phenyl pyrazole series was moderately active against extracellular bacteria. We identified the benzene amide ethers as an interesting series for further work. These new compound classes serve as starting points for the development of novel drugs to target intracellular M. tuberculosis.

microbiology↗

bioRxiv2020

InhA inhibitors have activity against non-replicating Mycobacterium tuberculosis

We previously identified a diazaborine series with potential for development as a new tuberculosis drug. This series has activity in vitro and in vivo and targets cell wall biosynthesis via inhibition of InhA. We tested the ability of two molecules of the diazaborine series to kill non-replicating Mycobacterium tuberculosis in the nutrient starvation model; both molecules were bactericidal, reducing viability by >3 logs in 21 days. Activity was not inoculum-dependent and showed similar kill rates to other InhA inhibitors (isoniazid and NITD-916). We conclude that inhibition of InhA is bactericidal against nutrient-starved non-replicating M. tuberculosis.

microbiology↗